LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
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NAME
Bio::EnsEMBL::RNAProduct - A class representing the mature RNA product of a transcript
DESCRIPTION
Objects of this class represent mature RNA products of transcripts. Examples of such products include MicroRNA (miRNA), circular RNA (circRNA) or piwi-interacting RNA (piRNA), and they commonly play a role in gene expression.
SYNOPSIS
my $rnaproduct = Bio::EnsEMBL::RNAProduct->new(
-SEQ_START => 36,
-SEQ_END => 58
);
$rnaproduct->stable_id('ENSS00090210');
my $start = $rnaproduct->start();
my $end = $rnaproduct->end();
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new
Arg [-SEQ_START] : The offset in the Transcript indicating the start
position of the product sequence.
Arg [-SEQ_END] : The offset in the Transcript indicating the end
position of the product sequence.
Arg [-START_EXON] : The Exon object in which the RNAProduct starts
Arg [-END_EXON] : The Exon object in which the RNAProduct ends
Arg [-STABLE_ID] : The stable identifier for this RNAPRoduct
Arg [-VERSION] : The version of the stable identifier
Arg [-DBID] : The internal identifier of this RNAProduct
Arg [-ADAPTOR] : The RNAProductAdaptor for this RNAProduct
Arg [-SEQ] : Manually sets the nucleotide sequence of this
RNAProduct. May be useful if this RNAProduct is not
stored in a database.
Arg [-CREATED_DATE] : the date the RNAProduct was created
Arg [-MODIFIED_DATE]: the date the RNAProduct was modified
Example : my $rp = Bio::EnsEMBL::RNAProduct->new(
-SEQ_START => 36,
-SEQ_END => 58
);
Description: Constructor. Creates a new RNAProduct object
Returntype : Bio::EnsEMBL::RNAProduct
Exceptions : none
Caller : general
Status : In Development
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add_Attributes
Arg [1..N] : Bio::EnsEMBL::Attribute $attribute
Attributes to add.
Example : $rnaproduct->add_Attributes($selenocysteine_attribute);
Description: Adds an Attribute to the RNAProduct.
If you add an attribute before you retrieve any from database,
lazy load will be disabled.
Returntype : none
Exceptions : throw on incorrect arguments
Caller : general
Status : Stable
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add_DBEntry
Arg [1] : Bio::EnsEMBL::DBEntry $dbe
The dbEntry to be added
Example : $rnaproduct->add_DBEntry($xref);
Description: Associates a DBEntry with this RNAProduct. Note that adding
DBEntries will prevent future lazy-loading of DBEntries for this
RNAProduct (see get_all_DBEntries).
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
Status : Stable
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cdna_end
Example : $rnaproduct_cdna_end = $rnaproduct->cdna_end();
Description : Returns the end position of the RNAProduct in cDNA
coordinates.
Since RNAProducts do not span multiple exons, this is
simply an alias for end().
Return type : Integer
Caller : General
Status : Stable
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cdna_start
Example : $rnaproduct_cdna_start = $rnaproduct->cdna_start();
Description : Returns the start position of the RNAProduct in cDNA
coordinates.
Since RNAProducts do not span multiple exons, this is
simply an alias for start().
Return type : Integer
Caller : General
Status : Stable
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created_date
Arg [1] : (optional) string $created_date - created date to set
Example : $rnaproduct->created_date('2007-01-10 20:52:00');
Description: Getter/setter for attribute created_date
Returntype : string
Exceptions : none
Caller : general
Status : Stable
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display_id
Example : print $rnaproduct->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For RNAProducts this is (depending on
availability and in this order) the stable ID, the dbID or an
empty string.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable
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end
Arg [1] : (optional) int $end - end position to set
Example : $rnaproduct->end(39);
Description: Getter/setter for the value of end, which is a position within
the precursor Transcript.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
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end_Exon
Arg [1] : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign
Example : $rnaproduct->end_Exon($exon1);
Description: Getter/setter for the value of end_Exon, which denotes the
exon at which RNAProduct ends.
Returntype : Bio::EnsEMBL::Exon
Exceptions : thrown on wrong argument type
Caller : general
Status : Stable
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genomic_end
Args : None
Example : $rnaproduct_genomic_end = $rnaproduct->genomic_end();
Description : Returns the end position of the RNAProduct in genomic
coordinates on the forward strand.
Return type : Integer
Exceptions : None
Caller : General
Status : Stable
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genomic_start
Args : None
Example : $rnaproduct_genomic_start = $rnaproduct->genomic_start();
Description : Returns the start position of the RNAProduct in
genomic coordinates on the forward strand.
Return type : Integer
Exceptions : None
Caller : General
Status : Stable
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get_all_Attributes
Arg [1] : optional string $attrib_code
The code of the attribute type to retrieve values for.
Example : ($n_attr) = @{$tl->get_all_Attributes('note')};
@rp_attributes = @{$rnaproduct->get_all_Attributes()};
Description: Gets a list of Attributes of this RNAProduct.
Optionally just get Attributes for given code.
Returntype : listref Bio::EnsEMBL::Attribute
Exceptions : none
Caller : general
Status : Stable
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get_all_DBEntries
Arg [1] : (optional) String, external database name,
SQL wildcard characters (_ and %) can be used to
specify patterns.
Arg [2] : (optional) String, external_db type,
('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : my @dbentries = @{ $rnaproduct->get_all_DBEntries() };
@dbentries = @{ $rnaproduct->get_all_DBEntries('Uniprot%') };
@dbentries = @{ $rnaproduct->get_all_DBEntries('%', 'ENSEMBL') };
Description: Retrieves DBEntries (xrefs) for this RNAProduct.
This method will attempt to lazy-load DBEntries
from a database if an adaptor is available and no
DBEntries are present on the RNAProduct (i.e. they
have not already been added or loaded).
Returntype : Listref to Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : ?
Status : Stable
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get_all_DBLinks
Arg [1] : (optional) String, database name
SQL wildcard characters (_ and %) can be used to
specify patterns.
Arg [2] : (optional) String, external database type, can be one of
('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : my @dblinks = @{ $rnaproduct->get_all_DBLinks() };
@dblinks = @{ $rnaproduct->get_all_DBLinks('mirbase%') };
@dblinks = @{ $rnaproduct->get_all_DBLinks('%', 'ENSEMBL') };
Description: This is here for consistancy with the Transcript
and Gene classes. It is a synonym for the
get_all_DBEntries() method.
Return type: Listref to Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : general
Status : Stable
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get_all_object_xrefs
Arg [1] : (optional) String, external database name
Arg [2] : (optional) String, external_db type
Example : @oxrefs = @{ $rnaproduct->get_all_object_xrefs() };
Description: Retrieves xrefs for this RNAProduct.
This method will attempt to lazy-load xrefs from a
database if an adaptor is available and no xrefs
are present on the RNAProduct (i.e. they have not
already been added or loaded).
NB: This method is an alias for the
get_all_DBentries() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable
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get_all_xrefs
Arg [1] : String database name (optional)
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : @xrefs = @{ $rnaproduct->get_all_xrefs() };
@xrefs = @{ $rnaproduct->get_all_xrefs('mirbase%') };
Description: This method is here for consistancy with the Gene
and Transcript classes. It is an alias for the
get_all_DBLinks() method, which in turn directly
calls get_all_DBEntries().
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable
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modified_date
Arg [1] : (optional) string $modified_date - modification date to set
Example : $rnaproduct->modified_date('2007-01-10 20:52:00');
Description: Getter/setter for attribute modified_date
Returntype : string
Exceptions : none
Caller : general
Status : Stable
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length
Example : print "RNA length =", $rnaproduct->length();
Description: Retrieves the length of the nucleotide sequence represented
by this RNAProduct object.
Returntype : int
Exceptions : none
Caller : webcode (protview etc.)
Status : Stable
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load
Arg [1] : Boolean $load_xrefs
Load (or don't load) xrefs. Default is to load xrefs.
Example : $rnaproduct->load();
Description : The Ensembl API makes extensive use of lazy-loading. Under some circumstances (e.g.,
when copying genes between databases), all data of
an object needs to be fully loaded. This method
loads the parts of the object that are usually
lazy-loaded.
Returns : none
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seq
Example : print $rnaproduct->seq();
Description: Retrieves a string representation of the nucleotide sequence
of this RNAProduct. This retrieves the transcript from the
database and gets its sequence, or retrieves the sequence which
was set via the constructor/setter.
Returntype : string
Exceptions : warning if the sequence is not set and cannot be retrieved from
the database.
Caller : webcode (protview etc.)
Status : Stable
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stable_id
Arg [1] : (optional) string $stable_id - stable ID to set
Example : $rnaproduct->stable_id('ENSS00090210');
Description: Getter/setter for attribute stable_id.
Unlike stable_id_version(), setting a new stable ID does NOT
reset the version number.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
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stable_id_version
Arg [1] : (optional) String - the stable ID with version to set
Example : $rnaproduct->stable_id("ENSS0059890.3");
Description: Getter/setter for stable id with version for this RNAProduct.
If the input string omits the version part, the version gets reset
to undef; use stable_id() if you want to avoid this.Returntype : String
Exceptions : none
Caller : general
Status : Stable
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start
Arg [1] : (optional) int $start - start position to set
Example : $rnaproduct->start(17);
Description: Getter/setter for the value of start, which is a position within
the precursor Transcript.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
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start_Exon
Arg [1] : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign
Example : $rnaproduct->start_Exon($exon1);
Description: Getter/setter for the value of start_Exon, which denotes the
exon at which RNAProduct starts.
Returntype : Bio::EnsEMBL::Exon
Exceptions : thrown on wrong argument type
Caller : general
Status : Stable
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summary_as_hash
Example : $rnaproduct_summary = $rnaproduct->summary_as_hash();
Description : Retrieves a textual summary of this RNAProduct.
Not inherited from Feature.
Returns : hashref of arrays of descriptive strings
Status : Intended for internal use
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synchronise_attributes
Example : $rnaproduct->synchronise_attributes();
Description : Some RNAProduct attributes, e.g. stem-loop arm in case
of MicroRNA, use a local cache of their value for convenience. Unless the corresponding setters update both
the cache value and the attribute (which would defeat
the convenience thing), we have to make sure the former
get propagated to the latter before storing the object
in the database:
- if no corresponding attribute exists, create one;
- if there is one, update its value.
Class-specific maps of attributes to synchronise are
provided by
RNAProductTypeMapper::class_attribute_cache_map() .
Returntype : none
Exceptions : throws if the object contains multiple attributes with the
given code and the choice which one to update is
ambiguous.
Caller : RNAProductAdaptor
Status : At Risk (In Development)
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transcript
Arg [1] : Transcript object (optional)
Description : Sets or retrieves the transcript object associated
with this RNAProduct object.
Exceptions : Throws if there is no adaptor or no dbID defined for
the RNAProduct object.
Returntype : Bio::EnsEMBL::Transcript
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type_code
Example : my $rp_type_code = $rnaproduct->type_code();
Description: Getter for the RNAProduct type (e.g. miRNA, circRNA, ...).
The type is expressed as human-readable code.
This is somewhat redundant because similar information can
be obtained simply by looking at the class of the object,
indeed type_code is not meant to be modified independently
of the class. However, there are certain use cases when the latter are more convenient than the former.
Returntype : string
Exceptions : none
Caller : ?
Status : In Development
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version
Arg [1] : (optional) string $version - version to set
Example : $rnaproduct->version(2);
Description: Getter/setter for attribute version
Returntype : string
Exceptions : none
Caller : general
Status : Stable
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